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  • C12Q1/701—Specific hybridization probes

Definitions

• Respiratory tract infections cause nearly half of the deaths due to infectious diseases in the United States (Wei, et al., Obstet Gynecol Clin North Am (2001) 28 (2): 283-304). About 75 percent of acute respiratory illnesses are caused by viruses.
• Human parainfluenza virus 1, human parainfluenza virus 2, human parainfluenza virus 3, respiratory syncytial virus, influenza virus A, influenza virus B, and adenovirus are the most common viruses that cause respiratory infections in both children and adults. Detection of these viruses is essential for diagnosis, prevention and treatment of respiratory diseases.
• the present invention relates to specific nucleic acid sequences for simultaneously detecting multiple respiratory viruses including human parainfluenza virus 1, human parainfluenza virus 2, human parainfluenza virus 3, respiratory syncytial virus, influenza virus A, influenza virus B, and adenovirus.
• this invention features a PCR primer set that contains two primer pairs for detecting two respiratory viruses, human parainfluenza virus 2 and adenovirus.
• One of the human parainfluenza virus 2 primers contains an oligo-nucleotide selected from the hemagglutinin-neuraminidase gene region (e.g., SEQ ID NO:5 or 6), and the other primer contains another oligo-nucleotide also selected from the same region (e.g., SEQ ID NO:7).
• One of the adenovirus primers contains an oligo-nucleotide selected from the hexon gene region, and the other primer contains another oligo-nucleotide also selected from the same region.
• the oligo-nucleotides in an adenovirus primer pair can be, SEQ ID NOs:24 and 26, SEQ ID NOs:24 and 27, or SEQ ID NOs:25 and 27.
• Each oligo-nucleotide has 14-40 (e.g., 14-35, 14-30, 14-25, or 14-20) nucleotides in length.
• the PCR primer set of this invention can further contain one or more additional specific primer pairs for detecting other respiratory viruses.
• one or more of the following five primer pairs can be included in the PCR primer set:
• this invention features a set of nucleic acids that contains one or more nucleic acids obtained from amplification of a group of respiratory virus nucleic acid templates with one of the PCR primer sets described above.
• the group of nucleic acid templates is prepared from one or more of the seven viruses mentioned above.
• the amplification products can be used as hybridization probes for virus detection.
• this invention features a probe set that can be used for detecting the seven respiratory viruses mentioned above.
• Each probe has 20-1,000 (e.g., 20-500, 20-200, or 20-50) nucleotides in length.
• the probe set contains one or more of the following:
• the probe set of this invention can further contain one or more of the following:
• Also within the scope of this invention is a method of simultaneously detecting respiratory viruses using a PCR primer set, a set of amplified nucleic acids, or a probe set described above.
• viruses to be detected are human parainfluenza virus 2 and adenovirus, and optionally, one or more of the following: human parainfluenza virus 1, human parainfluenza virus 3, respiratory syncytial virus, influenza virus A, and influenza virus B.
• the method includes (1) providing a nucleic acid from a sample suspected of containing a virus to be detected, (2) amplifying the nucleic acid with one of the PCR primer sets described above, and (3) detecting amplification products. Detection of an amplification product specific for a target virus indicates the presence of the target virus, and can be achieved by hybridizing the amplification products to one of the probe sets described above.
• kits for simultaneous detection of respiratory viruses including human parainfluenza virus 2 and adenovirus, and optionally, one or more of the following: human parainfluenza virus 1, human parainfluenza virus 3, respiratory syncytial virus, influenza virus A, and influenza virus B.
• the kit contains a PCR primer set, a set of amplified nucleic acids, a probe set described above, or any combination thereof. It may include other components such as a DNA polymerase, a PCR buffer, or a solid support on which one or more specific probes are immobilized.
• the present invention enables one to simultaneously detect as many as seven common respiratory viruses.
• the details of one or more embodiments of the invention are set forth in the accompanying description below. Other advantages, features, and objects of the invention will be apparent from the description, and from the claims.
• the present invention relates to simultaneous detection of two respiratory viruses, human parainfluenza virus 2 and adenovirus.
• a nucleic acid template prepared from a sample suspected of containing human parainfluenza virus 2 or adenovirus is amplified with a set of PCR primers, which contains a pair of human parainfluenza virus 2 primers and a pair of adenovirus primers.
• the amplification product if any, is detected by either gel electrophoresis and staining, or by probe hybridization. Detection of an amplification product specific for human parainfluenza virus 2 or adenovirus indicates the presence of that virus in the sample.
• the set of PCR primers can contain one or more additional primer pairs for detecting other respiratory viruses such as human parainfluenza virus 1, human parainfluenza virus 3, respiratory syncytial virus, influenza virus A, and influenza virus B.
• the nucleic acid template can be DNA (e.g., a genomic fragment or a restriction fragment) or RNA, in a purified or unpurified form. It can also be obtained from a biological sample, e.g., a specimen from a patient having symptoms of respiratory infection.
• the present invention features PCR primer pairs which can be used for simultaneously detecting the seven respiratory viruses mentioned above.
• the primer pairs for each virus are selected by analyzing virus sequences in GenBank using the DNAstar program (DNASTAR Inc., Madison, Wis. 53715, U.S.A.). A conserved region is first identified, followed by selection of primer pairs from this region.
• Each primer pair can be tested in a PCR using a nucleic acid template prepared from a patient diagnosed with infection of a virus to be detected to ensure that a specific amplification product is produced.
• the specificity of the primer pair should not be affected by the presence of other primer pairs, i.e., the same amplification product is produced.
• a primer pair selected for one virus preferably does not cause non-specific amplification of a nucleic acid template prepared from another virus, and amplification products specific for different viruses should be of different lengths.
• PCR primer pairs which can be used for simultaneously detecting the seven respiratory viruses mentioned above are as follows:
• each primer is listed in Table 1 below in Example 1.
• a primer is 14-40 nucleotides in length (PCR Application Manual, Boehringer Mannheim, 1995, page 37).
• specific virus sequences can be added to either the 5′-end or the 3′-end of each primer; non-specific sequences can be added to the 5′-end of each primer.
• An example of a non-specific sequence is a sequence containing a restriction site. Addition of such a sequence facilitates cloning of the amplification product.
• the present invention also features probes chosen from the regions amplified with primer pairs described above using the DNAstar program. Examples of the probes are as follows:
• each probe is listed in Table 3 below in Example 3.
• These probes, and longer probes containing them and having 20-1000 (e.g., 20-500, 20-200, and 20-50) nucleotides in length can be used for detecting the seven viruses mentioned above by hybridizing to unamplified target virus nucleic acids or target virus nucleic acids amplified with the above-described primer pairs.
• the amplification products described above are examples of such longer probes.
• GenBank search indicates that the nucleic acid sequences amplified with the primer pairs described above are specific for each of the seven viruses.
• a probe When a probe is combined with other probes for simultaneous detection of multiple viruses, the specificity of the probe should not be affected by the presence of other probes, i.e., it still hybridizes to the target virus nucleic acid.
• a probe selected for one virus does not hybridize to a nucleic acid prepared from another virus.
• the probes can be immobilized on the surface of a solid support, such as a membrane (a nylon-membrane or a nitrocellulose membrane), a glass, or a plastic polymer. Immobilization of probes to a membrane can be achieved by baking at 80° C. or UV cross-linking.
• the probes can also be covalently linked to a material (e.g., poly-lysine) coated on the surface of a glass.
• a novel method of immobilizing probes on a plastic polymer has recently been developed. See U.S. application Ser. No. 09/906,207.
• the probes can be synthesized de novo at precise positions on a solid substrate.
• a target amplification product described above can be detected by binding it to an immobilized probe.
• a labeled amplification product can be generated with a labeled amplification primer.
• the labeling can be done, chemically or enzymatically, after amplification.
• labeling reagents include, but are not limited to, a fluorescent molecule (e.g., fluorescein and rhodamine), a radioactive isotope (e.g., 32 P and 125 I), a calorimetric reagent, and a chemiluminescent reagent. Biotin and digoxgenin are frequently used for colorimetric detection on a membrane or a plastic polymer.
• Fluorescent labels such as Cy3 and Cy5 are widely used for detection on a glass.
• artificial tagging tails e.g., a protein or its antibody
• each virus nucleic acid template is only amplified with a primer pair selected for that particular virus. There is no non-specific amplification caused by the presence of other primer pairs.
• probes specific for different viruses are mixed together for simultaneous detection of the viruses, each target virus nucleic acid only hybridizes to a probe selected for that particular virus. There is no non-specific hybridization between a target virus nucleic acid and probes selected for other viruses.
• nucleotide variations are allowed in primers and probes described in this invention.
• single nucleotide polymorphisms may be associated with a particular genotype or phenotype, these primers and probes can be used to distinguish and categorize different virus strains.
• HN hemagglutinin-neuraminidase
• HPIV 2 sequences from GenBank Accession Nos af039930, af039931, af039932, af039934, af039937, x57559, af213353, af213354, d00865, and af213352 were analyzed using the DNAstar program. A conserved region was identified in the HN gene area. Two forward primers (PIV2-f929 and PIV2-f1015) and one reverse primer (PIV2-r1182) were selected from this conserved region (Table 1).
• RSV sequences from GenBank Accession Nos af035006, 63644, 50362, 50363, 11486, 74568, C — 001803, 39661, 39662, 00001, f013255, C — 001781, F013254, and 00736 were analyzed using the DNAstar program.
• a conserved region was identified in the non-structural protein 2 (NS 2) gene area.
• Two forward primers (RSV-f417 and RSV-fl 351) and two reverse primers (RSV-r641 and RSV-r1540) were selected from this conserved region (Table 1).
• INF A sequences from GenBank Accession Nos m12594, k00576, m12592, m12590, d30673, j02150, x52146, u08862, u65674, and u65670 were analyzed using the DNAstar program.
• a conserved region was identified in the non-structural protein (NS) gene area.
• Two forward primers (INFA-f1 and INFA-f2) and two reverse primers (INFA-r1 and INFA-r2) were selected from this conserved region (Table 1).
• INF B sequences from GenBank Accession Nos x13552, x00897, m18384, u70384, x13550, af101071, m58422, m58421, m65170, and k02713 were analyzed using the DNAstar program. A conserved region was identified in the hemagglutinin protein (HA) gene area. Two forward primers (INFB-92f and INFB-540f) and two reverse primers (INFB-384r and INFB-820r) were selected from this conserved region (Table 1).
• ADV sequences from GenBank Accession Nos x67709, ab053166, x76549, x84646, af065066,j01917, and j01966 were analyzed using the DNAstar program. A conserved region was identified in the Hexon protein (Hex) gene area. Two forward primers (ADV-f1 and ADV-f2) and two reverse primers (ADV-r1 and ADV-r2) were selected from this conserved region (Table 1).
• HPIV 1 sample numbers 580 and 4056
• HPIV 2 sample numbers 4855 and 5088
• HPIV 3 sample numbers 3116 and 3229
• RSV sample numbers 3116 and 3229
• INF A sample numbers NSW, PC, and DR
• INF B sample numbers 95, 96, 97, 98, 01
• ADV sample numbers 5456, 608, and 819.
• Throat swab specimens were collected from patients showing symptoms of virus infection, and were transferred to Hank's solution containing 0.2% BPA (p-borono-L-phenylalanine), 100 units of penicillin, 100 ⁇ g streptomycin, and 1.25 ⁇ g fungizone. Samples were kept at room temperature for 0.5-3 hours in emergency room before refrigerated at 4° C. or ⁇ 80° C.
• BPA p-borono-L-phenylalanine
• Monkey Kidney-2 cells were cultivated in a cell culture medium containing 2% FBS-MEM, 100 units of penicillin, 100 ⁇ g streptomycin, and 1.25 ⁇ g fungizone. Clinical specimens, 100 ⁇ l each, were inoculated into the cell culture medium and were incubated at 37 ⁇ , with CO 2 , for 7-10 days.
• Virus culture was centrifuged. Nucleic acids were isolated from 50 ⁇ l of the supernatant using the High Pure Viral Nucleic Acid Purification Kit (Roche), and were suspended in 20 ⁇ l DEPC-treated H 2 O.
• the Ready-To-Go RT-PCR Beads (Amersham Pharmacia Biotech Inc., U.S.A.) was dissolved in 35 ⁇ l DEPC-treated H 2 O. 7 ⁇ l of the solution were added to the pretreated nucleic acid mixture described above. The final mixture was incubated at 42 ⁇ for 45 min. Note that ADV is a DNA virus, thus the reverse transcription is not applicable.
• Each PCR tube contained 1 ⁇ l of 10X Taq DNA polymerase buffer, 0.3 ⁇ l of 25 mM MgCl 2 , 0.8 ⁇ l of 2.5 mM dNTPs (Promega, Madison, Wis., U.S.A.), 0.2 ⁇ l of 100 ⁇ M forward primer, 0.2 ⁇ l of 100 M reverse primer, 0.2 ⁇ l formamide, 5 ⁇ l of reverse transcription mixture, and 0.1 ⁇ l Taq DNA polymerase (5 units/ ⁇ l). dH 2 O was added to the mixture to bring the final volume to 10 ⁇ l.
• Peltier-effect Thermal Cyclers (PTC-100, MJ Research Inc., MA, U.S.A.) as follows: 95 ⁇ for 5 min; 35 cycles of 95 ⁇ for 40 sec, 50 ⁇ for 40 sec, and 72 ⁇ for 40 sec; and a final extension at 72 ⁇ for 5 min.
• Clinical samples used in this example were PIV 1 number 580, PIV2 number 5129, PIV3 number 1057, RSV number 3167, INF A number DR, INF B number 01, and ADV number 5456, provided by Dr. Shin-Ru-Shih (Chang Gung University, Tao Yuan, Taiwan).
• oligo-nucleotide primer mixture contained seven pairs of primers, one for each of the seven viruses (Table 2). The final concentration of each primer was 1 ⁇ M.
• a specific amplification product was detected in each sample, i.e., (1) a 268 bp fragment from amplification of the HPIV 1 template with primer set f834 and r1099, (2) a 168 bp fragment from amplification of the HPIV 2 template with primer set f1015 and r1182f, (3) a 156 bp fragment from amplification of the HPIV 2 template with primer set f904 and r1059, (4) a 222 bp fragment from amplification of the RSV template with primer set f417 and r641, (5) a 252 bp fragment from amplification of the INF A template with primer set INFA-12 and INFA-r2, (6) a 293 bp fragment from amplification of the INF B template with primer set 92f and 84r, and (7) a 556 bp fragment from amplification of the ADV template with primer set ADV-f1 and ADV-r1.
• Probes were selected from the amplified region of each virus genome using the DNAstar program (Table 3).
• HPIV 1 probes P1-1 5′-CTCCYTGCCYACTGTRAATGAGACTA-3′ (SEQ ID NO:28) P1-2 5′-CGAGTGAAGGTATAGAAGAYTTAGTATTTGACA-3′ (SEQ ID NO:29) P1-3 5′-CTCAAGGGAAAGACCAAATCTCATCG-3′ (SEQ ID NO:30) PIV1-P4 5′-GCTGCAGGAACAAGGGGTTATCAGTTATGC-3′ (SEQ ID NO:31) PIV1-P5 5′-GTGTAGGAAGRGGGATAAAYATTGAA-3′ (SEQ ID NO:32) PIV1-P6 5′-CCTTGGAGCGGAGTTGTTAAGCCACCG-3′ (SEQ ID NO:33) HPIV 2 probes P2-1 5′-GATCTAGCTGAACTGAGACTTGCTTTCTATTATTAT-3′ (SEQ ID NO:34) P2-2 5′-TCATATCTCTTCCAAAYACAACAGGGCA-3′
• Probes were spotted on a DR. PolymerTM Chip. Additional 5 to 20-mers of poly-T were attached to each of the probes before spotting. The probes were UV cross-linked to the surface of a DR. PolymerTM Chip. 4 positive detection controls, 4 positive PCR controls, 4 positive hybridization controls, and 4 negative controls were also spotted on the polymer chip.
• PCR products Prior to hybridization, 8 ⁇ l of PCR products were denatured for 5 minutes and mixed with 392 ⁇ l of DR. HybTM Hybridization Buffer-E. The mixture was added to the DR. PolymerTM Chip in a hybridization chamber and incubated at 50° C. for 1 hour. The chip was subsequently washed with 500 ⁇ l DR. Wash Buffer 5 times.
• Block Buffer Four hundred microliters of DR. Block Buffer were mixed with 0.2 ⁇ l streptavidin-AP (alkaline phosphatase). The mixture was added to the DR. PolymerTM Chip in a hybridization chamber, and was incubated for 30 minutes at room temperature. The chip was subsequently washed with DR. Wash Buffer 5 times.
• Detection Buffer Three hundred and ninety-two microliters of DR. Detection Buffer were mixed with 8 ⁇ l NBT/BCIP. The mixture was added to the DR. PolymerTM Chip in a hybridization chamber, and was incubated for 10 minutes in a dark room. The chip was subsequently washed twice with DR. Wash Buffer prior to color development.
• each probe specifically designed for a particular virus was able to capture the amplification product produced from the template isolated from the target virus sample, i.e., (1) color developed at P1-1, P1-2, P1-3, PIV1-P4, PIV1-P5, and PIV1-P6 spots when the probes were hybridized to HPIV 1 amplification products; (2) color developed at P2-1P2-2, and P2-3 spots when the probes were hybridized to HPIV 2 amplification products; (3) color developed at P3-1, P3-2, and P3-3 spots when the probes were hybridized to HPIV 3 amplification products; (4) color developed at R-1, R-2, R-3, R-10, R-4, and a mixture of R-71 and R-72 spots when the probes were hybridized to RSV amplification products; (5) color developed at A1, A2, and A3 spots when the probes were hybridized to INF A amplification products; (6) color developed at B1, B2, and B3 spots when the probes were hybridized to INF B a

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